Skip to content

[WIP] Use better latex symbolics option #1227

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 3 commits into
base: master
Choose a base branch
from
Open

[WIP] Use better latex symbolics option #1227

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
1c10a9d
init
TorkelE Apr 11, 2025
fe2fc45
up
TorkelE Apr 12, 2025
917c318
Merge branch 'master' into latex_symbol_update
TorkelE Apr 12, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 4 additions & 2 deletions src/dsl.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,13 @@ macro species(ex...)
lastarg = vars.args[end]

# start adding metadata statements where the vector of symbols was previously declared
# adds `[latexwrapper = string]` metadata which improves latexify printing.
idx = length(vars.args)
resize!(vars.args, idx + length(lastarg.args) + 1)
for sym in lastarg.args
vars.args[idx] = :($sym = ModelingToolkit.wrap(setmetadata(
ModelingToolkit.value($sym), Catalyst.VariableSpecies, true)))
vars.args[idx] = :($sym = ModelingToolkit.wrap(setmetadata(setmetadata(
ModelingToolkit.value($sym), Catalyst.VariableSpecies, true),
Symbolics.SymLatexWrapper, string)))
idx += 1
end

Expand Down
4 changes: 2 additions & 2 deletions src/reactionsystem.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1445,7 +1445,7 @@ function MT.flatten(rs::ReactionSystem; name = nameof(rs))
end

function complete_check(sys, method)
if MT.iscomplete(sys)
if MT.iscomplete(sys)
error("$method with one or more `ReactionSystem`s requires systems to not be marked complete, but system: $(MT.get_name(sys)) is marked complete.")
end
nothing
Expand Down Expand Up @@ -1506,7 +1506,7 @@ function ModelingToolkit.extend(sys::MT.AbstractSystem, rs::ReactionSystem;

complete_check(sys, "ModelingToolkit.extend")
complete_check(rs, "ModelingToolkit.extend")

any(T -> sys isa T, (ReactionSystem, ODESystem, NonlinearSystem)) ||
error("ReactionSystems can only be extended with ReactionSystems, ODESystems and NonlinearSystems currently. Received a $(typeof(sys)) system.")

Expand Down
39 changes: 21 additions & 18 deletions src/reactionsystem_serialisation/serialisation_support.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -150,6 +150,7 @@ x_2_string(x::Symbol) = ":$x"
x_2_string(x::Number) = string(x)
x_2_string(x::Pair) = "$(x_2_string(x[1])) => $(x_2_string(x[2]))"
x_2_string(x::Nothing) = "nothing"
x_2_string(x::Function) = String(Symbol(x))
function x_2_string(x::Vector)
output = "["
for val in x
Expand Down Expand Up @@ -212,30 +213,32 @@ end

# List of all recognised metadata (we should add as many as possible), and th keyword used to declare
# them in code.
const RECOGNISED_METADATA = Dict([Catalyst.ParameterConstantSpecies => "isconstantspecies"
Catalyst.VariableBCSpecies => "isbcspecies"
Catalyst.VariableSpecies => "isspecies"
Catalyst.EdgeParameter => "edgeparameter"
Catalyst.CompoundSpecies => "iscompound"
Catalyst.CompoundComponents => "components"
Catalyst.CompoundCoefficients => "coefficients"
ModelingToolkit.VariableDescription => "description"
ModelingToolkit.VariableBounds => "bounds"
ModelingToolkit.VariableUnit => "unit"
ModelingToolkit.VariableConnectType => "connect"
ModelingToolkit.VariableNoiseType => "noise"
ModelingToolkit.VariableInput => "input"
ModelingToolkit.VariableOutput => "output"
ModelingToolkit.VariableIrreducible => "irreducible"
ModelingToolkit.VariableStatePriority => "state_priority"
ModelingToolkit.VariableMisc => "misc"
ModelingToolkit.TimeDomain => "timedomain"])
const RECOGNISED_METADATA = Dict([Catalyst.ParameterConstantSpecies => "isconstantspecies",
Catalyst.VariableBCSpecies => "isbcspecies",
Catalyst.VariableSpecies => "isspecies",
Catalyst.EdgeParameter => "edgeparameter",
Catalyst.CompoundSpecies => "iscompound",
Catalyst.CompoundComponents => "components",
Catalyst.CompoundCoefficients => "coefficients",
ModelingToolkit.VariableDescription => "description",
ModelingToolkit.VariableBounds => "bounds",
ModelingToolkit.VariableUnit => "unit",
ModelingToolkit.VariableConnectType => "connect",
ModelingToolkit.VariableNoiseType => "noise",
ModelingToolkit.VariableInput => "input",
ModelingToolkit.VariableOutput => "output",
ModelingToolkit.VariableIrreducible => "irreducible",
ModelingToolkit.VariableStatePriority => "state_priority",
ModelingToolkit.VariableMisc => "misc",
ModelingToolkit.TimeDomain => "timedomain",
Symbolics.SymLatexWrapper => "latexwrapper"])

# List of metadata that does not need to be explicitly declared to be added (or which is handled separately).
const SKIPPED_METADATA = [
Catalyst.VariableSpecies,
ModelingToolkit.MTKVariableTypeCtx,
ModelingToolkit.SymScope,
Symbolics.SymLatexWrapper,
Symbolics.VariableDefaultValue,
Symbolics.VariableSource]

Expand Down
67 changes: 58 additions & 9 deletions test/visualisation/latexify.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ raw"\begin{align*}
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")

Expand All @@ -88,10 +88,10 @@ raw"\begin{align*}
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")

# Latexify.@generate_test latexify(rn, mathjax = false)
@test latexify(rn, mathjax = false) == replace(
raw"\begin{align*}
Expand All @@ -109,7 +109,7 @@ raw"\begin{align*}
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")
end
Expand All @@ -127,7 +127,7 @@ let
raw"\begin{align*}
\varnothing &\xrightleftharpoons[d_{a}]{\frac{p_{a} B^{n}}{k^{n} + B^{n}}} \mathrm{A} \\
\varnothing &\xrightleftharpoons[d_{b}]{p_{b}} \mathrm{B} \\
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
\end{align*}
", "\r\n"=>"\n")

Expand All @@ -136,7 +136,7 @@ raw"\begin{align*}
raw"\begin{align*}
\varnothing &\xrightleftharpoons[d_{a}]{\frac{p_{a} B^{n}}{k^{n} + B^{n}}} \mathrm{A} \\
\varnothing &\xrightleftharpoons[d_{b}]{p_{b}} \mathrm{B} \\
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
\end{align*}
", "\r\n"=>"\n")
end
Expand All @@ -150,7 +150,7 @@ let
# Latexify.@generate_test latexify(rn)
@test latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{p} (m + n)\mathrm{X}
\varnothing &\xrightarrow{p} (m + n)\mathrm{X}
\end{align*}
", "\r\n"=>"\n")
end
Expand Down Expand Up @@ -241,7 +241,7 @@ let
# Latexify.@generate_test latexify(rn)
@test latexify(rn) == replace(
raw"\begin{align*}
\mathrm{Y} &\xrightarrow{Y k} \varnothing
\mathrm{Y} &\xrightarrow{Y k} \varnothing
\end{align*}
", "\r\n"=>"\n")
end
Expand All @@ -258,7 +258,7 @@ let
@test latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightleftharpoons[\frac{d}{V\left( t \right)}]{\frac{p}{V\left( t \right)}} \mathrm{X} \\
\frac{\mathrm{d} V\left( t \right)}{\mathrm{d}t} &= X\left( t \right) - V\left( t \right)
\frac{\mathrm{d} V\left( t \right)}{\mathrm{d}t} &= X\left( t \right) - V\left( t \right)
\end{align*}
", "\r\n"=>"\n")
end
Expand All @@ -280,3 +280,52 @@ let
# Latexify.@generate_test latexify(extended, mathjax=false)
@test_broken false
end

# Checks that the `SymLatexWrapper` metadata option is correctly added to all symbolics created
# by the DSL. Checks that this is also the case for species created through the `@species` macro.
# Currently only implemented for species.
let
# Via the DSL (@reaction_network).
rn1 = @reaction_network begin
@species Y(t)
@variables W(t)
@parameters p
@equations D(V) ~ - V
k1, 0 --> X
end
@test_broken all(hasmetadata(u, Symbolics.SymLatexWrapper) && (getmetadata(u, Symbolics.SymLatexWrapper) == string) for u in unknowns(rn1))
@test_broken all(hasmetadata(p, Symbolics.SymLatexWrapper) && (getmetadata(p, Symbolics.SymLatexWrapper) == string) for p in parameters(rn1))

# Via the DSL but using `begin .. end` in declarations and additional options.
rn2 = @reaction_network begin
@species begin
X(t)
Y(t), [description = "A species"]
Z(t) = 1.0
end
@variables begin
V(t)
W(t), [description = "A variable"]
U(t) = 2.0
end
@parameters begin
k1
q, [description = "A parameter"]
r = 3.0
end
@equations D(V) ~ - V
k1, 0 --> X
end
@test_broken all(hasmetadata(u, Symbolics.SymLatexWrapper) && (getmetadata(u, Symbolics.SymLatexWrapper) == string) for u in unknowns(rn2))
@test_broken all(hasmetadata(p, Symbolics.SymLatexWrapper) && (getmetadata(p, Symbolics.SymLatexWrapper) == string) for p in parameters(rn2))

# Via the DSL (@reaction).
rx = @reaction p, 0 --> x
@test_broken hasmetadata(rx.rate, Symbolics.SymLatexWrapper) && (getmetadata(rx.rate, Symbolics.SymLatexWrapper) == string)
@test hasmetadata(rx.products[1], Symbolics.SymLatexWrapper) && (getmetadata(rx.products[1], Symbolics.SymLatexWrapper) == string)

# Via the @species.
t = default_t()
@species XYZ(t)
@test hasmetadata(XYZ, Symbolics.SymLatexWrapper) && (getmetadata(XYZ, Symbolics.SymLatexWrapper) == string)
end
Loading